+++ /dev/null
-/*
- * mergefilecommand.cpp
- * Mothur
- *
- * Created by Pat Schloss on 6/14/09.
- * Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "mergefilecommand.h"
-
-//**********************************************************************************************************************
-vector<string> MergeFileCommand::setParameters(){
- try {
- CommandParameter pinput("input", "String", "", "", "", "", "",false,true); parameters.push_back(pinput);
- CommandParameter poutput("output", "String", "", "", "", "", "",false,true); parameters.push_back(poutput);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "MergeFileCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string MergeFileCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The merge.file command takes a list of files separated by dashes and merges them into one file.";
- helpString += "The merge.file command parameters are input and output.";
- helpString += "Example merge.file(input=small.fasta-large.fasta, output=all.fasta).";
- helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "MergeFileCommand", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-MergeFileCommand::MergeFileCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["merge"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-MergeFileCommand::MergeFileCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- if(option == "help") {
- help();
- abort = true; calledHelp = true;
- }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
-
- //check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["merge"] = tempOutNames;
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
- if (inputDir == "not found"){ inputDir = ""; }
-
- string fileList = validParameter.validFile(parameters, "input", false);
- if(fileList == "not found") { m->mothurOut("you must enter two or more file names"); m->mothurOutEndLine(); abort=true; }
- else{ m->splitAtDash(fileList, fileNames); }
-
- //if the user changes the output directory command factory will send this info to us in the output parameter
- string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found") { outputDir = ""; }
-
-
- numInputFiles = fileNames.size();
- ifstream testFile;
- if(numInputFiles == 0){
- m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) + " file names"); m->mothurOutEndLine();
- abort=true;
- }
- else{
- for(int i=0;i<numInputFiles;i++){
- if (inputDir != "") {
- string path = m->hasPath(fileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { fileNames[i] = inputDir + fileNames[i]; }
- }
-
- if(m->openInputFile(fileNames[i], testFile)){ abort = true; }
- testFile.close();
- }
- }
-
- outputFileName = validParameter.validFile(parameters, "output", false);
- if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine(); abort=true; }
- else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName); }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int MergeFileCommand::execute(){
- try {
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- ofstream outputFile;
- m->openOutputFile(outputFileName, outputFile);
-
- char c;
- for(int i=0;i<numInputFiles;i++){
- ifstream inputFile; //declaration must be inside for loop of windows throws an error
-
- m->openInputFile(fileNames[i], inputFile);
-
- while(!inputFile.eof()){
- if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); m->mothurRemove(outputFileName); return 0; }
-
- c = inputFile.get();
- //-1 is eof char
- if (int(c) != -1) { outputFile << c; }
- }
-
- inputFile.close();
- }
-
- outputFile.close();
-
- if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
- m->mothurOutEndLine();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "MergeFileCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
projects / mothur.git / blobdiff